// get_arg.h
//

#if !defined(GETARG_H)
#define GETARG_H

#include <string>
//#include <iosfwd>
#include <sstream>
#include <string>
#include <vector>
#include <iostream>
#include <fstream>

#include <program_options_helper.h>

class t_program_args : public program_options_helper::t_std_program_args_with_errors
{
	friend
	bool process_command_line_options(int argc, char* argv[], t_program_args& args);
public:
	std::string				results_summary;
	bool					output_ds_only;
	bool					output_dn_only;
	bool					output_ds_coverage;
	float					dn_threshold;
	float					ds_threshold;
	float					tau_threshold;
	unsigned				len_threshold;
	float					fragment_coverage;
	float					residues_coverage;
	bool					coverage_both;
	std::string				file_input;
	std::string				comment_letters;
};

bool process_command_line_options(int argc, char* argv[], t_program_args& args);
#endif //GETARG_H
